CHIKV 28dpi scRNA-seq
Ryan Sheridan
2024-01-18
UMAP projections show sample groups (left), cell type annotations (middle), and CHIKV+ cells (right).
The fraction of cells passing QC filtering cutoffs is shown for each sample.
The fraction of CHIKV+ cells passing QC filtering cutoffs is shown for each sample.
Macrophages
Subset annotations
UMAP projections show macrophage subsets
Module scores for Culemann et al. gene lists are shown for each macrophage cluster. Clusters are colored based on the assigned subset labels.
Heatmaps show mean expression of Culemann et al. gene lists. Replicates are shown separately for each macrophage subset.
CCR2_ARG1_infiltrating
CCR2_IL1B_infiltrating
CX3CR1_lining
RELMa_interstitial
AQP1_interstitial
CHIKV+ cells
UMAP projections show CHIKV+ cells (left) and CHIKV-high clusters (middle, right) for CHIKV-infected samples.
The fraction of cells that are CHIKV+ is shown for each replicate from each macrophage subset. P values were calculated by pooling replicates together, using a hypergeometric test with Bonferroni correction.
Differential expression
Top upregulated genes associated with inflammatory disease are shown below for mock- vs CHIKV-infected macrophages.
Top genes upregulated in CHIKV-infected mice are shown below for each macrophage subset.
AQP1_interstitial
CX3CR1_lining
infiltrating
RELMa_interstitial
unassigned
Simmons et al.Â
SLAMF7_stim
SLAMF7_high
arthritis
T cells
Genes upregulated in T cells from CHIKV vs mock-infected mice are shown below. All CD4+ or CD8+ T cells were grouped together.
Ifng expression is shown below for each T cell subset
